**1. Introduction**

The human gastrointestinal tract is one of the most complex and diverse ecosystem known, with a plethora of fungi, viruses, bacteria and protists. This community of commensals usually dominated by bacteria is often referred to as microbiota, and their collective genome is termed the microbiome. The gu<sup>t</sup> microbiota play critical role in the health of the host, which include but is not limited to the maturation of the immune system, the prevention of pathogenic infection, the alteration of intestinal morphology and angiogenesis, the fermentation of undigested polysaccharides and the synthesis and conversion of bioactive compounds [1–4].

Perturbations or dysbiosis of the gu<sup>t</sup> microbiota as a result of diet, drug intake or environmental changes can result in severe health challenges with fatal outcomes. Diseases such as irritable bowel syndrome (IBS); obesity; inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease; cancer; and inflammatory disorders (diseases associated with abnormal function of the immune system and chronic inflammation) are associated with the perturbation of the gu<sup>t</sup> microbiota [5,6]. An array of other diseases, such as neurodegenerative disorders (Alzheimer's disease and the autism spectrum disorder), chronic kidney disease, diabetes and atherosclerotic cardiovascular disease, as summarized in Table 1, have been linked to the dysbiosis of the gu<sup>t</sup> [7–9]. The focus of this review is centered on gastrointestinal diseases associated with the alteration of the gu<sup>t</sup> microbiota, and recent technologies used in the study of gastrointestinal microbiota, with the view to identifying their potential applications in clinical practice.


